If you're only paying attention to the movies, Megatron's Evil Scheme Flowchart gots lots of holes and makes little sense. But if you follow the fifty million movie-based novels and comic series, it's put together somewhat reasonably. (Mostly thanks to John Barber, who is kind of awesome.) If you want to see how Megatron's Evil Scheme Flowchart works in the "expanded universe," TFWiki.net's "Movie timeline" page puts everything into amazing detail. Chris McFeely put it together (and continues to maintain it) and it was so awesome that it was last month's Featured Article.

But, yeah, going only by the movies themselves, it's kind of a mess.

EDIT: Okay, I thought I could get away with just posting this here without a huge disclaimer that I'm not saying this "fixes" the movie, or that people should be required to know this stuff or whatever bullshit like that. I just thought it was interesting supplementary material. Additional reading, were one to be so inclined.